if (!require('knitr')) install.packages('knitr'); library('knitr')
knitr::opts_chunk$set(warning=FALSE, message=FALSE, fig.align='center')

# Load in packages
if (!require("pacman")) install.packages("pacman"); library(pacman) # for rapid install if not in library

# load packages
pacman::p_load("RgoogleMaps", "SDMTools", "rgdal", "ggmap", "gridExtra", "automap", "cowplot","sp", "gstat", "plotrix", "dplyr", "ggplot2", "scales","magrittr","plyr","effects", "ggpubr", "sjstats", "RColorBrewer")

Background

Hakalau National Forest Wildlife Refuge Isoscapes
Data collected 20-21 August 2019 in Hakalau Forest, Hawai’i Island. plants and plant samples collected from afforested/restored plots after a century of deforestation from cattle grazing (now, koa plantations or KP sites) and remnant mixed koa-ohia forests (RK sites). Target engineers of forest habitats are Acacia koa (Hawaiian name: Koa), an indigenous hardwood species that forms native forest canopies and associates with nitrogen fixing bacteria. Understory species include Rubus argutus – an invasive species (common name: sawtooth blackberry) – and an endemic species Rubus hawaiiensis (common name: ’Ākala); both are members of the Roseaceae family. Noteably, R. argutus was found more in the remnant plot (i.e., RK) and the indigenous R. hawaiiensis was common in the restored plot (i.e, KP).

Plants samples were collected in a spatially explicit fashion (every 4 or 5m) with a 20 x 35m superplot, consisting of thirty-five 4 x 5m subplots. This data was used to create a δ13C and δ15N stable isotope landscape, hereafter ‘isoscape’. Koa and Rubus spp. were collected within each 4 x 5m subplot.

Plot densities were…
KP: Koa (18 trees) Rubus (14 plants) per 20 x 35m plot= 0.026 Koa m-2, 0.020 Rubus m-2 RK: Koa (10 trees) Rubus (28 plants) per 20 x 35m plot= 0.014 Koa m-2, 0.040 Rubus m-2

Site Maps

# load data
HKP.gps<-read.csv("data/Hakalau.gps.csv")
API<-read.csv("data/API_key.csv")
API.key<-API[1,1]

#quick map
# ggplot(HKP.gps, aes(x = longitude, y = latitude)) + coord_quickmap() + geom_point()

######## using ggmap
register_google(key=API.key)

########
#Hawaiian islands Map
########
hi_map<-get_map(location=c(-157,20.5),zoom=7,maptype="satellite",color="color")
hi_map_for_man <- ggmap(hi_map) +
  geom_point(aes(x = -155.320, y = 19.83), pch=23,colour="black",fill="red", size = 2, stroke=0.5) +
  xlab("") + ylab("Latitude") +
  scale_y_continuous(limits=c(18.8, 22.2))+
  scale_x_continuous(limits=c(-160.2, -154)) +
  theme(axis.text=element_text(colour="black",size=5),
        axis.title=element_text(colour="black",size=8),
        plot.margin = unit(c(0, 0.5, 0, 0.7), "cm")) +
  ggsn::scalebar(x.min=-160.2, x.max=-154, y.min=18.8, y.max=22.2, dist=50, dist_unit="km", transform=TRUE,
                 st.bottom=FALSE, st.size=2, box.fill=c("gray50", "white"), model="WGS84",st.color="white", border.size=0.5)


##########
# site map plot showing distance from plots
##########
HKP.rev=c(-155.317, 19.82158002)

map2<-get_map(HKP.rev, 
                      zoom=16, 
                      scale = 2, 
                      maptype= "satellite",
                      source="google", extent= "device", legend="topright")

###
###### site single point only
site.only<-HKP.gps[c(1,5),]

Hakalau.site<-
  ggmap(map2)+
  geom_point(aes(x=longitude, y=latitude), data=site.only, alpha=0.5, color="white", size=4)+
  labs(x="", y="") +
  scale_y_continuous(limits=c(19.81785, 19.8242))+
  scale_x_continuous(limits=c(-155.3223, -155.311)) +
  theme(text = element_text(size=6),
       plot.margin = unit(c(0.2, 0.5, 0.2, 0.2), "cm")) +
  annotate("text", x=-155.3187, y=19.8225, label= "KP", size=3, col="white") +
  annotate("text", x=-155.31478, y=19.8224, label= "RK", size=3, col="white") +
ggsn::scalebar(x.min=-155.314, x.max=-155.311, y.min=19.818, y.max=19.824, dist=100, 
               dist_unit="m", transform=TRUE,
              st.bottom=FALSE, st.size=2, box.fill=c("gray50", "white"), model="WGS84",st.color="white", border.size=0.5)


##########
# Site plots: KP or RK only
##########
KP<- HKP.gps[(HKP.gps$Site=="KP"),]
RK<- HKP.gps[(HKP.gps$Site=="RK"),]

####### KP map
KP.gps<-c(-155.3189, lat=19.8219)
mapKP<-get_map(KP.gps,
              zoom=19, 
              scale = 2, 
              maptype= "satellite",
              source="google", extent= "device", legend="topright")

KP.map<-ggmap(mapKP, group=type)+
  geom_point(aes(x=longitude, y=latitude, shape=type, color=type), data=KP, alpha=0.5, size=3)+
  scale_y_continuous(limits=c(19.82165, 19.82225))+
  scale_x_continuous(limits=c(-155.3194, -155.3183)) +
  theme(legend.position="top",
    legend.text = element_text(color = "white"),
    legend.title = element_text(color = "white"),
    legend.key = element_rect(fill = "white"),
    plot.margin = unit(c(0, 0.5, 0, 0), "cm"),
    text = element_text(size=8)) +
  guides(colour= guide_legend(override.aes = list(color = "white"))) +
  scale_color_manual(values=c('red','mediumseagreen'))+
  labs(x="Longitude", y="Latitude") +
  annotate("text", x=-155.31923, y=19.82225, label= "Restored Forest (KP)", size=3, col="white")+
  ggsn::scalebar(x.min=-155.3183, x.max=-155.3187, y.min=19.82165, y.max=19.82225, dist=10, 
               dist_unit="m", transform=TRUE,
              st.bottom=FALSE, st.size=2, box.fill=c("gray50", "white"), model="WGS84", st.color="white", border.size=0.5)


####### RK map
RK.edit<-RK[-12,] # remove "proximate" Koa
RK.edit[9,3]<-"koa" # rename to be "koa"

RK.gps<-c(-155.315, 19.8216)
mapRK<-get_map(RK.gps,
               zoom=19, 
               scale = 2, 
               maptype= "satellite",
               source="google", extent= "device", legend="topright")

RK.map<-ggmap(mapRK, group=type)+
  geom_point(aes(x=longitude, y=latitude, shape=type, color=type), data=RK.edit, alpha=0.5, size=3)+
  scale_color_manual(values=c('red','mediumseagreen', "dodgerblue"))+
  scale_shape_manual(values=c(16, 17, 3)) +
  scale_y_continuous(limits=c(19.82120, 19.82195))+
  scale_x_continuous(limits=c(-155.31575, -155.3144)) +
  theme(legend.position="top",
        legend.title=element_blank(), 
        legend.key = element_rect(fill = "white"),
        plot.margin = unit(c(0, 0.5, 0, 0), "cm"), 
        text = element_text(size=8)) +
  labs(x="Longitude", y="") +
  annotate("text", x=-155.31555, y=19.821925, label= "Remnant Forest (RK)", size=3, col="white")+
  ggsn::scalebar(x.min=-155.3148, x.max=-155.3144, y.min=19.8212, y.max=19.8219, dist=10, 
               dist_unit="m", transform=TRUE,
              st.bottom=FALSE, st.size=2, box.fill=c("gray50", "white"), model="WGS84", st.color="white", border.size=0.5)


site.plots<-plot_grid(hi_map_for_man, Hakalau.site, KP.map, RK.map, 
          labels=c('A', 'B', 'C', 'D'), label_size=8, hjust=-1, vjust= 2, ncol=2, nrow=2)
site.plots
Figure 1. Site map of (a) the Hawaiian Island archipelago, (b) sampling plot in Hakalau Forest Refuge, and (c) plot layouts, highlighting *Acacia koa* density.

Figure 1. Site map of (a) the Hawaiian Island archipelago, (b) sampling plot in Hakalau Forest Refuge, and (c) plot layouts, highlighting Acacia koa density. 

### export it
pdf(file= "figures/Fig 1.sitemaps.pdf", height=5, width=8)
site.plots
dev.off()

Ecology and Isotopes data

  • DBH calculations
  • data mutating
HKP.df<-read.csv("data/Hakalau.rawdata.csv")

########## DBH 
DBH.df<- HKP.df %>%
  select(c(DBH..cm.1, DBH..cm.2, DBH..cm.3, DBH..cm.4, DBH..cm.5))

# replace NAs with zeros
DBH.df<- DBH.df %>%
  mutate_each(funs(replace(., which(is.na(.)), 0)))

# if only one trunk, then make new column and report this value
DBH.df <- DBH.df %>%
  mutate(DBH.1trunk = ifelse(DBH..cm.2>"0", 0, DBH..cm.1))

# if multiple trunks, sum of squares and square root all trunks
# and plug in the DBH for single trunks
DBH.df <- DBH.df %>%
  mutate(DBH.Total = ifelse(DBH.1trunk=="0",  
                     sqrt(DBH..cm.1^2 + DBH..cm.2^2 + DBH..cm.3^2 + DBH..cm.4^2 + DBH..cm.5^2), DBH.1trunk))

# replace zeros with NA now that total DBH has been calculated
DBH.df$DBH.Total<-as.numeric(ifelse(DBH.df$DBH.Total=="0", "NA", DBH.df$DBH.Total))

############ Canopy diameter
# use area of an elipse, a x b x π, where a and b are major and minor radius
Can.df<-HKP.df %>%
  select(c(canopy.0..m, canopy.90..m, canopy.180..m, canopy.270..m))

# Major radius is the average of 0 and 180 degrees
Can.df<- Can.df %>% 
  mutate(Maj.rad = rowMeans(cbind(canopy.0..m, canopy.180..m), na.rm=T))

# Minor radius is the average of 90 and 270 degrees
Can.df<- Can.df %>% 
  mutate(Min.rad = rowMeans(cbind(canopy.90..m, canopy.270..m), na.rm=T))

# Elipse area
Can.df<- Can.df %>% 
  mutate(Canopy.area = ifelse(Maj.rad>0, Maj.rad*Min.rad*3.14, "NA"))

########################
# combine DBH.Total and Canopy.area with isotope dataframe and reduce columns
HKP.df$DBH.Total<-DBH.df$DBH.Total
HKP.df$Canopy.area<-Can.df$Canopy.area

# HKP.data is the full dataframe
HKP.data<- HKP.df %>%
  select(c(Plot, Position.point, Sample, DBH.Total, Canopy.area, d15N, d13C, N..percent, Total.N..mmol.gdw, C..percent, Total.C..mmol.gdw, C.N))

write.csv(HKP.data, "data/Hakalau.fulldata.csv")

Rubus and Koa relationship

  • plotting the relationship between Rubus and Koa d15N
  • took average of 3 closest Koa trees to each Rubus plant
  • plot Rubus d15N against Koa d15N (mean of 3 trees)
Ndfa<-read.csv("data/Ndfa.Rub.csv")

# rename the d15N so we know it is for rubus
Ndfa$d15N.Rub<-Ndfa$d15N
Ndfa$d15N.Koa<-Ndfa$mean.d15N.Ndfa

####################
#################### relationship between koa and rubus d15N?
# Yes, but a bit stronger in the RK site
mod.KP<-lm(Ndfa[(Ndfa$Plot=="KP"),]$d15N.Rub~Ndfa[(Ndfa$Plot=="KP"),]$d15N.Koa); anova(mod.KP)
summary(mod.KP)
int.rubKP<-coef(summary(mod.KP))[1] #intercept
slop.rubKP<-coef(summary(mod.KP))[2] #slope
                                  
mod.RK<-lm(Ndfa[(Ndfa$Plot=="RK"),]$d15N.Rub~Ndfa[(Ndfa$Plot=="RK"),]$d15N.Koa); anova(mod.RK)
summary(mod.RK)
int.RKoa<-coef(summary(mod.RK))[1] #intercept
slop.RKoa<-coef(summary(mod.RK))[2] #slope

## ranges
# RK Koa and Rubus
(max(Ndfa[(Ndfa$Plot=="RK"),]$d15N.Koa)-min(Ndfa[(Ndfa$Plot=="RK"),]$d15N.Koa))
(max(Ndfa[(Ndfa$Plot=="RK"),]$d15N.Rub)-min(Ndfa[(Ndfa$Plot=="RK"),]$d15N.Rub))

# KP Koa and Rubus
(max(Ndfa[(Ndfa$Plot=="KP"),]$d15N.Koa)-min(Ndfa[(Ndfa$Plot=="KP"),]$d15N.Koa))
(max(Ndfa[(Ndfa$Plot=="KP"),]$d15N.Rub)-min(Ndfa[(Ndfa$Plot=="KP"),]$d15N.Rub))


#### plot
BW.back<-theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black", size=0.2))

Rub.Koa.d15N.plot<-ggplot(data=Ndfa, aes(x=d15N.Koa, y=d15N.Rub, color=Plot))+
  geom_point(aes(color=Plot), alpha=.8) + 
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  coord_equal() + theme_bw() +
  xlab(expression(paste(italic("Acacia koa "), delta^{15}, N, " (\u2030)"), sep=""))+
  ylab(expression(paste(italic("Rubus"), " spp. ", delta^{15}, N, " (\u2030)"), sep="")) +
  guides(colour=guide_legend(override.aes = list(stroke=1, fill="NA", alpha=1))) +
  geom_smooth(method = "lm", alpha = .15, size=0.6) +
  theme(legend.title = element_blank(),
        axis.text=element_text(size=6),
        axis.title=element_text(size=10),
        legend.position = c(0.85, 0.94), legend.key.size = unit(0.4, "cm"),
        legend.text = element_text(size = 8), legend.background=element_blank()) +
  annotate(geom="text", x=2.45, y=0.8, 
           label=expression(paste("KP:  R"^{2},"= 0.27, ",italic("p"), "=0.056")), size=2) +
  annotate(geom="text", x=2.45, y=0.6, 
           label=expression(paste("RK:  R"^{2},"= 0.26, ",italic("p="), bold("0.006"))), size=2) +
  BW.back

Rub.Koa.d15N.plot
Figure 2a. Relationship between d15N-Koa and 15N-Rubus at two sampling sites.

Figure 2a. Relationship between d15N-Koa and 15N-Rubus at two sampling sites. 

dev.copy(pdf, "figures/Fig 3.Koa.Rub.regr.pdf", width=4, height=4, encod="MacRoman")
dev.off()

DBH, Canopy d15N models

  • plot against d15N values with model curves
  • scatters with models
  • d15N differ by PLOT (KP vs RK), no other effects or relationship with DBH or Canopy
# ** No relationship between d15N and DBH or Canopy at plot level**
# ** Effects at PLOTs on d15N (lower in KP) **


######## plot of d15N and DBH, and d15N and Canopy area

# all samples
par(mfrow=c(1,2), mar=c(4,5,1,1))

#### DBH
mod.DBH<-lm(d15N~DBH.Total*Plot, data=HKP.data) # no interaction effect

mod.DBH<-lm(d15N~DBH.Total+Plot, data=HKP.data)
int<-coef(summary(mod.DBH))[1]
DBH.slope<-coef(summary(mod.DBH))["DBH.Total",1] # DBH (slope for all figures)
RK.int<-coef(summary(mod.DBH))["PlotRK",1] # RK, KP = 0


# no significant relationship to d15N but a trend for DECREASE with DBH
plot(d15N~DBH.Total, data=HKP.data,
    col=c("coral","dodgerblue")[as.factor(Plot)],
    pch=c(1,2)[as.factor(Plot)],
    ylab=expression(paste(delta^{15}, N, " (\u2030, air)")),
    xlab="DBH (cm)",
    ylim=c(0,5), xlim=c(0,60))
    ablineclip(int, DBH.slope, col="coral", lwd=2, 
               x1 = min(HKP.data$DBH.Total[HKP.data$Plot=="KP"], na.rm=T), 
               x2 = max(HKP.data$DBH.Total[HKP.data$Plot=="KP"], na.rm=T)) # KP model
    ablineclip((int+ RK.int), DBH.slope, col="dodgerblue", lwd=2, 
               x1 = min(HKP.data$DBH.Total[HKP.data$Plot=="RK"], na.rm=T), 
               x2 = max(HKP.data$DBH.Total[HKP.data$Plot=="RK"], na.rm=T)) # RK model

    
#### Canopy
mod.Can<-lm(d15N~Canopy.area*Plot, data=HKP.data) # no interaction

mod.Can<-lm(d15N~Canopy.area+Plot, data=HKP.data)
int<-coef(summary(mod.Can))[1]
Can.slope<-coef(summary(mod.Can))["Canopy.area",1] # DBH (slope for all figures)
RK.int<-coef(summary(mod.Can))["PlotRK",1] # RK, KP = 0

# no significant relationship to d15N but a trend for INCREASE with canopy area
plot(d15N~Canopy.area, data=HKP.data, yaxt="n",
     col=c("coral","dodgerblue")[as.factor(Plot)],
     pch=c(1,2)[as.factor(Plot)],
     xlab=expression(paste("Canopy (m"^2,")")),
     ylab="", 
     ylim=c(0,5), xlim=c(0,80))
     axis(side=2, labels=F)
     ablineclip(int, Can.slope, col="coral", lwd=2, 
               x1 = min(HKP.data$Canopy.area[HKP.data$Plot=="KP"], na.rm=T), 
               x2 = max(HKP.data$Canopy.area[HKP.data$Plot=="KP"], na.rm=T)) # KP model
     ablineclip((int+ RK.int), Can.slope, col="dodgerblue", lwd=2, 
               x1 = min(HKP.data$Canopy.area[HKP.data$Plot=="RK"], na.rm=T), 
               x2 = max(HKP.data$Canopy.area[HKP.data$Plot=="RK"], na.rm=T)) # RK model
     legend("topright", legend=levels(HKP.data$Plot), box.lty=0, bg="transparent", lty=1, pch=c(1,2), 
            col=c("coral", "dodgerblue"), cex=1)

dev.copy(pdf, "figures/d15N.DBH.Canopy.pdf", width=7, height=5, encod="MacRoman")
dev.off()

With Plot being most important effect, divide DBH and Canopy to be plot mean +/- SE
Supplemental Figure 1. with afforested and remnant forests
- DBH and Canopy figure as bar chart and means - using Mann-Whitney nonparametric tests: significant plot effects - greater DBH (KP), trend for greater Canopy (RK)

## Models
mod.DBH<-lm(DBH.Total~Plot, data=HKP.data); anova(mod.DBH) # signif
## Analysis of Variance Table
## 
## Response: DBH.Total
##           Df Sum Sq Mean Sq F value  Pr(>F)   
## Plot       1 1290.6 1290.58   8.369 0.00762 **
## Residuals 26 4009.5  154.21                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
mod.Can<-lm(Canopy.area~Plot, data=HKP.data); anova(mod.Can) # not signif, a bit wobbly in assumptions
## Analysis of Variance Table
## 
## Response: Canopy.area
##           Df Sum Sq Mean Sq F value Pr(>F)
## Plot       1  654.2  654.16  2.0862 0.1606
## Residuals 26 8152.6  313.56
# diagnostic plots
for(i in c(4:5)){
  Y<-HKP.data[,i]
  full<-lm(Y~Plot, data=HKP.data, na.action=na.exclude)
  R <- resid(full) #save glm residuals
  op<-par(mfrow = c(2,3), mar=c(5,4,1,2), pty="sq")
  plot(full, add.smooth = FALSE, which=1)
  QQ <- qqnorm(R, main = colnames(HKP.data)[i]) 
  QQline <- qqline(R)
  hist(R, xlab="Residuals", main = colnames(HKP.data)[i])
  plot(HKP.data$Plot, R, xlab=colnames(HKP.data)[i], ylab="Residuals")
}
# Mann-Whitney U-Test
mwu(HKP.data, DBH.Total, Plot) # signif
## 
## # Mann-Whitney-U-Test
## 
## Groups 1 = KP (n = 18) | 2 = RK (n = 10):
##   U = 315.000, W = 144.000, p = 0.010, Z = 2.589
##   effect-size r =  0.489
##    rank-mean(1) = 17.50
##    rank-mean(2) =  9.10
mwu(HKP.data, Canopy.area, Plot) # not
## 
## # Mann-Whitney-U-Test
## 
## Groups 1 = KP (n = 18) | 2 = RK (n = 10):
##   U = 252.000, W = 81.000, p = 0.666, Z = -0.432
##   effect-size r =  0.082
##    rank-mean(1) = 14.00
##    rank-mean(2) = 15.40
#### plots
DBH.m<-aggregate(DBH.Total~Plot, data=HKP.data, mean)
Can.m<-aggregate(Canopy.area~Plot, data=HKP.data, mean)
canopy.mean<-aggregate(Canopy.area~Plot, data=HKP.data, sum) 

DBH.SE<-aggregate(DBH.Total~Plot, data=HKP.data, std.error)
Can.SE<-aggregate(Canopy.area~Plot, data=HKP.data, std.error)

DBH.n<-aggregate(DBH.Total~Plot, data=HKP.data, length)
Can.n<-aggregate(Canopy.area~Plot, data=HKP.data, length)

mean.eco<-cbind(DBH.m, Can.m[2], DBH.SE[2], Can.SE[2]); colnames(mean.eco)<-c("Plot", "DBH", "Can", "D.SE", "C.SE")

pd <- position_dodge(0.7) #offset for error bars

BW.back2<-theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black", size=0.4))

### DBH plot of mean/SE by plot
DBH.plot<-ggplot(data=mean.eco, aes(x=Plot, y=DBH))+
  geom_bar(stat="identity", position = pd, width=0.7, fill="gray70")+
  geom_errorbar(aes(ymin=DBH-D.SE, ymax=DBH+D.SE), size=.5, width=0, position=pd) +
  xlab("Plots") +
  ylab("dbh (cm)") + 
  theme(legend.title = element_blank(),
        axis.text=element_text(size=6),
        axis.title=element_text(size=8))+
  annotate(geom="text", x=1.5, y=35, label=expression(paste(bold("*"))), size=4) +
  BW.back2

### Canopy plot of mean/SE by plot
Canopy.plot<-ggplot(data=mean.eco, aes(x=Plot, y=Can))+
  geom_bar(stat="identity", position = pd, width=0.7, fill="gray70")+
  geom_errorbar(aes(ymin=Can-C.SE, ymax=Can+C.SE), size=.5, width=0, position=pd) +
  xlab("Plots") +
  ylab(expression(paste("Canopy (m"^2,")"))) + 
  theme(legend.title = element_blank(),
        axis.text=element_text(size=6),
        axis.title=element_text(size=8))+
  BW.back2

#  figures together
plot_grid(DBH.plot, Canopy.plot,
     labels=c('A', 'B'), label_size=8, hjust=-1, vjust= 3, ncol=2, nrow=1)

dev.copy(pdf, "figures/FigS1.DBHCanopy.pdf", width=4, height=3.5, encod="MacRoman")
dev.off()

Run statistics on the responses (dd15N, 13C, tissue C and N)

# models
## tests for assumptions
for(i in c(6:12)){
  Y<-HKP.data[,i]
  full<-lm(Y~Plot+Sample, data=HKP.data, na.action=na.exclude)
  R <- resid(full) #save glm residuals
 
  op<-par(mfrow = c(2,3), mar=c(5,4,1,2), pty="sq")
  plot(full, add.smooth = FALSE, which=1)
  QQ <- qqnorm(R, main = colnames(HKP.data)[i]) 
  QQline <- qqline(R)
  hist(R, xlab="Residuals", main = colnames(HKP.data)[i])
  plot(HKP.data$Plot, R, xlab=colnames(HKP.data)[i], ylab="Residuals")
  plot(HKP.data$Sample, R, xlab=colnames(HKP.data)[i], ylab="Residuals")
}
########## Separate dataframes
# make a factor for "plants" or "soil"
HKP.data<-HKP.data %>%
  mutate(Sample.Type = ifelse(Sample=="Soil", "Soil", "Plants"))

#all plants
plants<-HKP.data[(HKP.data$Sample.Type=="Plants"),]

# make level to contrast Koa vs Rubus spp
plants<-plants %>%
  mutate(Plant.Type = ifelse(Sample=="Koa", "Koa", "Rubus spp"))

#only Koa
Koa<-HKP.data[(HKP.data$Sample=="Koa"),]

#only Rubus
Rubus<-HKP.data[(HKP.data$Sample=="RUBARG" | HKP.data$Sample=="RUBHAW"),]

# only KP (or RK) and only plants in those sites
KP.df<-HKP.data[(HKP.data$Plot=="KP"),]; KP.df.plants<-KP.df[(KP.df$Sample.Type=="Plants"),]
RK.df<-HKP.data[(HKP.data$Plot=="RK"),]; RK.df.plants<-RK.df[(RK.df$Sample.Type=="Plants"),]

d15N models

######## Nitrogen isotopes
d15N.plants<-lm(d15N~Plot, data=plants); anova(d15N.plants) # plants signif.
## Analysis of Variance Table
## 
## Response: d15N
##           Df Sum Sq Mean Sq F value   Pr(>F)    
## Plot       1 23.774 23.7737  30.484 5.71e-07 ***
## Residuals 68 53.031  0.7799                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d15N.plants))
d15N.Koa<-lm(d15N~Plot, data=Koa); anova(d15N.Koa) # Koa signif.
## Analysis of Variance Table
## 
## Response: d15N
##           Df  Sum Sq Mean Sq F value  Pr(>F)  
## Plot       1  4.7952  4.7952  7.4173 0.01139 *
## Residuals 26 16.8088  0.6465                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d15N.Koa))
d15N.Rubus<-lm(d15N~Plot, data=Rubus); anova(d15N.Rubus) # Rubus signif.
## Analysis of Variance Table
## 
## Response: d15N
##           Df  Sum Sq Mean Sq F value    Pr(>F)    
## Plot       1  9.9155  9.9155  13.768 0.0006289 ***
## Residuals 40 28.8076  0.7202                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d15N.Rubus))
# only in KP
# only comparing the 2 plant species 
d15N.KP<-lm(d15N~Sample, data=KP.df.plants); anova(d15N.KP) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: d15N
##           Df  Sum Sq Mean Sq F value  Pr(>F)  
## Sample     1  2.9463 2.94632  6.0621 0.01978 *
## Residuals 30 14.5807 0.48602                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d15N.KP)) 
# only in RK
# only comparing the 2 plant species 
d15N.RK<-lm(d15N~Sample, data=RK.df.plants); anova(d15N.RK) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: d15N
##           Df  Sum Sq Mean Sq F value  Pr(>F)  
## Sample     1  4.4682  4.4682  5.1829 0.02886 *
## Residuals 36 31.0357  0.8621                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d15N.RK))

d13C models

######## ######## 
######## Carbon isotopes
d13C.plants<-lm(d13C~Plot, data=plants); anova(d13C.plants) # plants signif.
## Analysis of Variance Table
## 
## Response: d13C
##           Df Sum Sq Mean Sq F value   Pr(>F)    
## Plot       1  44.33  44.330  81.164 3.25e-13 ***
## Residuals 68  37.14   0.546                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d13C.plants))
d13C.Koa<-lm(d13C~Plot, data=Koa); anova(d13C.Koa) # Koa signif.
## Analysis of Variance Table
## 
## Response: d13C
##           Df Sum Sq Mean Sq F value    Pr(>F)    
## Plot       1 12.825 12.8250  21.018 0.0001006 ***
## Residuals 26 15.865  0.6102                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d13C.Koa))
d13C.Rubus<-lm(d13C~Plot, data=Rubus); anova(d13C.Rubus) # Rubus signif.
## Analysis of Variance Table
## 
## Response: d13C
##           Df Sum Sq Mean Sq F value    Pr(>F)    
## Plot       1 21.848 21.8484  46.101 3.684e-08 ***
## Residuals 40 18.957  0.4739                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d13C.Rubus))
d13C.KP<-lm(d13C~Sample, data=KP.df.plants); anova(d13C.KP) #only koa vs. rubus comparision
## Analysis of Variance Table
## 
## Response: d13C
##           Df Sum Sq Mean Sq F value Pr(>F)
## Sample     1  0.851 0.85100  1.2075 0.2806
## Residuals 30 21.142 0.70474
plot(allEffects(d13C.KP))
d13C.RK<-lm(d13C~Sample, data=RK.df.plants); anova(d13C.RK) #only koa vs. rubus comparision
## Analysis of Variance Table
## 
## Response: d13C
##           Df  Sum Sq Mean Sq F value  Pr(>F)  
## Sample     1  1.4676 1.46758  3.8622 0.05714 .
## Residuals 36 13.6796 0.37999                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(d13C.RK))

Nitrogen content models

####### Nitrogen content
TN.plants<-lm(Total.N..mmol.gdw~Plot, data=plants); anova(TN.plants) # plants not signif by plot
## Analysis of Variance Table
## 
## Response: Total.N..mmol.gdw
##           Df Sum Sq  Mean Sq F value Pr(>F)
## Plot       1 0.0315 0.031547   0.377 0.5413
## Residuals 68 5.6904 0.083683
plot(allEffects(TN.plants))
TN.Koa<-lm(Total.N..mmol.gdw~Plot, data=Koa); anova(TN.Koa) # Koa not signif by plot
## Analysis of Variance Table
## 
## Response: Total.N..mmol.gdw
##           Df  Sum Sq  Mean Sq F value Pr(>F)
## Plot       1 0.03271 0.032711  0.5942 0.4478
## Residuals 26 1.43136 0.055052
plot(allEffects(TN.Koa))
TN.Rubus<-lm(Total.N..mmol.gdw~Plot, data=Rubus); anova(TN.Rubus) # Rubus trend by plot
## Analysis of Variance Table
## 
## Response: Total.N..mmol.gdw
##           Df Sum Sq Mean Sq F value  Pr(>F)  
## Plot       1 0.2110 0.21100  3.6973 0.06164 .
## Residuals 40 2.2828 0.05707                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(TN.Rubus))
N.KP<-lm(Total.N..mmol.gdw~Sample, data=KP.df.plants); anova(N.KP) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: Total.N..mmol.gdw
##           Df Sum Sq Mean Sq F value    Pr(>F)    
## Sample     1 1.5930  1.5930  36.455 1.254e-06 ***
## Residuals 30 1.3109  0.0437                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(N.KP)) 
N.RK<-lm(Total.N..mmol.gdw~Sample, data=RK.df.plants); anova(N.RK) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: Total.N..mmol.gdw
##           Df  Sum Sq Mean Sq F value  Pr(>F)  
## Sample     1 0.38328 0.38328  5.7415 0.02189 *
## Residuals 36 2.40323 0.06676                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(N.RK))

Carbon content models

######## ######## 
######## Carbon content
TC.plants<-lm(Total.C..mmol.gdw~Plot, data=plants); anova(TC.plants) # plants signif.
## Analysis of Variance Table
## 
## Response: Total.C..mmol.gdw
##           Df Sum Sq Mean Sq F value Pr(>F)
## Plot       1   1.08  1.0809  0.2279 0.6346
## Residuals 68 322.45  4.7420
plot(allEffects(TC.plants))
TC.Koa<-lm(Total.C..mmol.gdw~Plot, data=Koa); anova(TC.Koa) # Koa signif.
## Analysis of Variance Table
## 
## Response: Total.C..mmol.gdw
##           Df  Sum Sq Mean Sq F value Pr(>F)
## Plot       1  0.0377 0.03768  0.0962 0.7589
## Residuals 26 10.1849 0.39173
plot(allEffects(TC.Koa))
TC.Rubus<-lm(Total.C..mmol.gdw~Plot, data=Rubus); anova(TC.Rubus) # Rubus signif.
## Analysis of Variance Table
## 
## Response: Total.C..mmol.gdw
##           Df  Sum Sq Mean Sq F value   Pr(>F)   
## Plot       1  34.074  34.074  8.6486 0.005419 **
## Residuals 40 157.595   3.940                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(TC.Rubus))
C.KP<-lm(Total.C..mmol.gdw~Sample, data=KP.df.plants); anova(C.KP) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: Total.C..mmol.gdw
##           Df  Sum Sq Mean Sq F value    Pr(>F)    
## Sample     1 122.081 122.081  473.95 < 2.2e-16 ***
## Residuals 30   7.728   0.258                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(C.KP)) 
C.RK<-lm(Total.C..mmol.gdw~Sample, data=RK.df.plants); anova(C.RK) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: Total.C..mmol.gdw
##           Df  Sum Sq Mean Sq F value Pr(>F)  
## Sample     1  32.592  32.592  7.3308 0.0103 *
## Residuals 36 160.052   4.446                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(C.RK))

C:N models

####### C:N content
CN.plants<-lm(C.N~Plot, data=plants); anova(CN.plants) # not signif.
## Analysis of Variance Table
## 
## Response: C.N
##           Df Sum Sq Mean Sq F value Pr(>F)
## Plot       1   5.95  5.9547  0.6628 0.4184
## Residuals 68 610.89  8.9837
CN.Koa<-lm(C.N~Plot, data=Koa); anova(CN.Koa) # not signif.
## Analysis of Variance Table
## 
## Response: C.N
##           Df  Sum Sq Mean Sq F value Pr(>F)
## Plot       1   2.289  2.2886  0.3456 0.5617
## Residuals 26 172.171  6.6220
CN.Rubus<-lm(C.N~Plot, data=Rubus); anova(CN.Rubus) # not signif
## Analysis of Variance Table
## 
## Response: C.N
##           Df Sum Sq Mean Sq F value Pr(>F)
## Plot       1   4.27  4.2660  0.5037  0.482
## Residuals 40 338.78  8.4694
CN.KP<-lm(C.N~Sample, data=KP.df.plants); anova(CN.KP) #only koa vs. rubus comparision, signif.
## Analysis of Variance Table
## 
## Response: C.N
##           Df Sum Sq Mean Sq F value   Pr(>F)   
## Sample     1  75.46  75.460  12.771 0.001214 **
## Residuals 30 177.26   5.909                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(allEffects(CN.KP)) 
CN.RK<-lm(C.N~Sample, data=RK.df.plants); anova(CN.RK) #only koa vs. rubus comparision, not signif
## Analysis of Variance Table
## 
## Response: C.N
##           Df Sum Sq Mean Sq F value Pr(>F)
## Sample     1  24.48  24.482  2.6413 0.1128
## Residuals 36 333.68   9.269
plot(allEffects(CN.RK))

Figure 2
data means and SE for plots
- bar plots of d13C, d15N, TC and TN for all 4 samples types with asterisks for significant effects

## make some means and SE
d13C.m<-aggregate(d13C~Plot+Sample, data=HKP.data, mean)
d15N.m<-aggregate(d15N~Plot+Sample, data=HKP.data, mean)
TN.m<-aggregate(Total.N..mmol.gdw~Plot+Sample, data=HKP.data, mean)
TC.m<-aggregate(Total.C..mmol.gdw~Plot+Sample, data=HKP.data, mean)
CN.m<-aggregate(C.N~Plot+Sample, data=HKP.data, mean)

d13C.SE<-aggregate(d13C~Plot+Sample, data=HKP.data, std.error)
d15N.SE<-aggregate(d15N~Plot+Sample, data=HKP.data, std.error)
TN.SE<-aggregate(Total.N..mmol.gdw~Plot+Sample, data=HKP.data, std.error)
TC.SE<-aggregate(Total.C..mmol.gdw~Plot+Sample, data=HKP.data, std.error)
CN.SE<-aggregate(C.N~Plot+Sample, data=HKP.data, std.error)

d13C.n<-aggregate(d13C~Plot+Sample, data=HKP.data, length)
d15N.n<-aggregate(d15N~Plot+Sample, data=HKP.data, length)

mean.data<- cbind(d13C.m, d15N.m[3], TN.m[3], TC.m[3], d13C.SE[3], d15N.SE[3], TN.SE[3], TC.SE[3], CN.m[3], CN.SE[3])
colnames(mean.data)<-c("Plot", "Sample", "d13C.mean", "d15N.mean", "TN.mean", "TC.mean", "d15N.SE", "d13C.SE", "TN.SE", "TC.SE", "CN.mean", "CN.SE")

# rename Rubus species for plotting
levels(mean.data$Sample)[levels(mean.data$Sample)=="RUBARG"] <- "Rubus spp"
levels(mean.data$Sample)[levels(mean.data$Sample)=="RUBHAW"] <- "Rubus spp"

mean.data$Sample<-factor(mean.data$Sample, levels=c("Soil", "Koa", "Rubus spp"))

### make mean plots
pd <- position_dodge(0.7) #offset for error bars

### d13C
d13C.plot<-ggplot(data=mean.data, aes(x=Sample, y=d13C.mean, fill=Plot, group=Plot))+
  geom_bar(stat="identity", position = pd, width=0.7, alpha=0.5)+
  geom_errorbar(aes(ymin=d13C.mean-d13C.SE, ymax=d13C.mean+d13C.SE), size=.3, width=0, position=pd) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  scale_x_discrete(labels=expression(Soil, italic(A.~koa),italic(Rubus)~spp.))+
  annotate(geom="text", x=1, y=-27.5, label=expression(paste(bold("*"))), size=4) +
  annotate(geom="text", x=2, y=-33, label=expression(paste(bold("*"))), size=4) +
  annotate(geom="text", x=3, y=-33, label=expression(paste(bold("*"))), size=4) +
  theme(text = element_text(size=8)) +
  ylab(expression(paste(delta^{13}, C, " (\u2030, V-PDB)"))) + BW.back2

### d15N
d15N.plot<-ggplot(data=mean.data, aes(x=Sample, y=d15N.mean, fill=Plot, group=Plot))+
  geom_bar(stat="identity", position = pd, width=0.7, alpha=0.5) + ylim(c(0,8)) +
  geom_errorbar(aes(ymin=d15N.mean-d15N.SE, ymax=d15N.mean+d15N.SE), size=.3, width=0, position=pd) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  scale_x_discrete(labels=expression(Soil, italic(A.~koa),italic(Rubus)~spp.))+
  theme(text = element_text(size=8)) +
  annotate(geom="text", x=2, y=2.8, label=expression(paste(bold("*"))), size=4) +
  annotate(geom="text", x=3, y=3.3, label=expression(paste(bold("*"))), size=4) +
  ylab(expression(paste(delta^{15}, N, " (\u2030, air)"))) + BW.back2

### total Carbon
TC.plot<-ggplot(data=mean.data, aes(x=Sample, y=TC.mean, fill=Plot, group=Plot))+
  geom_bar(stat="identity", position = pd, width=0.7, alpha=0.5)+ ylim(c(0, 60)) +
  geom_errorbar(aes(ymin=TC.mean-TC.SE, ymax=TC.mean+TC.SE), size=.3, width=0, position=pd) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  scale_x_discrete(labels=expression(Soil, italic(A.~koa),italic(Rubus)~spp.))+
  theme(text = element_text(size=8),
        legend.position = c(0.9, 0.9), legend.key.size = unit(0.3, "cm"),
        legend.title = element_blank()) +
  annotate(geom="text", x=1, y=25, label=expression(paste(bold("*"))), size=4) +
  annotate(geom="text", x=3, y=42, label=expression(paste(bold("*"))), size=4) +
  ylab("Total Carbon (mmol/gdw)") +  BW.back2 

### total Nitrogen
TN.plot<-ggplot(data=mean.data, aes(x=Sample, y=TN.mean, fill=Plot, group=Plot))+
  geom_bar(stat="identity", position = pd, width=0.7, alpha=0.5)+
  geom_errorbar(aes(ymin=TN.mean-TN.SE, ymax=TN.mean+TN.SE), size=.3, width=0, position=pd) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  scale_x_discrete(labels=expression(Soil, italic(A.~koa),italic(Rubus)~spp.))+
  theme(text = element_text(size=8)) +
  ylab("Total Nitrogen (mmol/gdw)") + BW.back2

# get the legend, # create some space to the left of the legend
bar.legend <- get_legend(
  TN.plot + 
    theme(legend.box.margin = margin(0, 0, 0, 12)) +
    theme(legend.title=element_blank())+ # no need for a title above legend
    theme(legend.key.size = unit(0.3, "cm")))

#  figures together
bar.plots<-plot_grid(d15N.plot + theme(legend.position = "none"), 
                     d13C.plot + theme(legend.position = "none"),
                     TN.plot + theme(legend.position = "none"),
                     TC.plot,
                     nrow=1, ncol=4, labels=c('A', 'B', 'C', 'D'), 
          label_size=8, hjust=-1, vjust= 3)

#plot_grid(bar.plots, bar.legend, rel_widths = c(8, 1)) # legend  1/8 size as first obj.
bar.plots

dev.copy(pdf, "figures/Fig 2.mean.data.sample.pdf", width=7.5, height=3, encod="MacRoman")
dev.off()

ISO-KRIG

Give the data a “krig-over”.

First, make krigs of the full plot and all data layers

# load data
krig<-read.csv("data/krig.matrix.csv") # matrix of points for isoscape grid


# merge kriging data with isotope data
data.merge<-as.data.frame(join_all(list(HKP.data, krig), by = "Position.point", type='full'))

data.merge<-data.merge[c(-167:-194),] # drop NAs where no samples tKPen
scape.data<-data.merge

write.csv(scape.data, "output/scape.data.csv")

#################

δ15N pooled isoscape

setup

################# d15N krigs
################# make site maps based on bubble plots
set.seed(100)

# just KP site
krig.KP<- scape.data %>% filter(Plot=="KP")
krig.KP$Sample<-droplevels(krig.KP$Sample)

# modify one point slightly due to overlap of coordinate system
krig.KP$y.matrix[24]=2.4; krig.KP$y.meter[24]=2.4
krig.KP$x.matrix[24]=5.4; krig.KP$x.meter[24]=5.4

KP.map<-krig.KP %>% as.data.frame %>% 
  ggplot(aes(x.meter, y.meter, group=Sample)) + geom_point(aes(size=d15N, color=Sample), alpha=3/4) + 
  ggtitle("KP plot--d15N (permil)") + coord_equal() + theme_bw()

# just RK site
krig.RK<- scape.data %>% filter(Plot=="RK")
krig.RK$Sample<-droplevels(krig.RK$Sample)

RK.map<-krig.RK %>% as.data.frame %>% 
  ggplot(aes(x.meter, y.meter, group=Sample)) + geom_point(aes(size=d15N, color=Sample), alpha=3/4) +
  ggtitle("RK plot--d15N (permil)") + coord_equal() + theme_bw()

plot_grid(RK.map, KP.map, ncol=2, nrow=1)
dev.copy(pdf, "figures/notused/dot.scape.pdf", width=9, height=4, encod="MacRoman")
dev.off()

#####################
#####################

First generate an isoscape for the compelte pooled sample set: the soil, koa, and Rubus. Do this for each of the two forests. Figure 4ab

Acacia koa plantation (KP) δ15N isoscape

## Krig KP sites
coordinates(krig.KP)<- ~x.meter + y.meter

# Create a grid of "Pixels" using x as columns and y as rows
# And the rows and columns of pixels:
Columns=seq(from=-1, to=36, by=0.05)
Rows=seq(from=-1, to=21, by=0.05)
Grid.KP <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.KP) <- ~ x+y
gridded(Grid.KP) <- TRUE # Plot the grid and points

## expand binding box 
#krig.KP@bbox # current data binding box
x<-c(-1, 36)
y<-c(-1, 21)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
krig.KP@bbox<-bbox(S) # expanded binding box for data
Grid.KP@bbox<-bbox(S) # expand for plot corner

# autokrige
d15N.KP.auto <- autoKrige(d15N ~ 1, krig.KP, Grid.KP) # ordinary kriging
plot(d15N.KP.auto, sp.layout = list(pts = list("sp.points", krig.KP)))

#d15N.KP.auto$krige_output

# make to dataframes for lm, combine
KP.pred.N <- d15N.KP.auto[1] %>% as.data.frame() # model predictions
KP.df.N <- krig.KP %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.KP.df.N<- left_join(KP.df.N, KP.pred.N, by = c("x.meter"="krige_output.x")) # longest axis is x
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.KP.df.N)
summary(mod) #R squared = 0.21

mean(pred.KP.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 4.4 d15N
mean(pred.KP.df.N$krige_output.var1.stdev, na.rm=T) # 2.1

# inspect model
# plot(pred.KP.df.N$krige_output.var1.pred ~ pred.KP.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

### map in automap
#automapPlot(d15N.KP.auto$krige_output, "var1.pred", sp.layout = list("sp.points", krig.KP, pch=16, col="gray20", cex=0.5), col.regions=my.palette)

# map in ssplot
# note that the prediction "var1.pred" component of the krig is a SpatialPixelsDataFrame. Need to call the krig, then the component df("krige_output"), then the output column ("var1.pred") to plot in spplot

# variance
# spplot(d15N.KP.auto$krige_output,"var1.stdev")

#predicted krige
my.palette2 <- brewer.pal(n = 6, name = "BuGn")
my.palette3 <- colorRampPalette(c("firebrick1", "darkseagreen1", "azure1"))(4)
col.scheme.N <- colorRampPalette(my.palette3)


plotd15N.krig.KP<-spplot(d15N.KP.auto$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", krig.KP, pch=c(16,17,1)[krig.KP$Sample], 
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{15}, N, " - KP (Restored Forest)")), cex=0.8), colorkey=FALSE)


###########################

Remnant Forest (RK) δ15N isoscape

###########################
# RK Site Krig
###########################
## Krig RK site 
krig.RK<- scape.data %>% filter(Plot=="RK")
krig.RK$Sample<-droplevels(krig.RK$Sample)


coordinates(krig.RK)<- ~x.meter + y.meter

Columns=seq(from=-1, to=21, by=0.05)
Rows=seq(from=-1, to=36, by=0.05)
Grid.RK <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.RK) <- ~ x+y
gridded(Grid.RK) <- TRUE # Plot the grid and points

## expand binding box 
#krig.RK@bbox # current data binding box
x<-c(-1, 21)
y<-c(-1, 36)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
Grid.RK@bbox<-bbox(S) # expand for plot corner

# autokrige
# 'fix.values' = The items describe the fixed value for the nugget (y-intercept), range (of interprolation) and sill(asymptote) respectively. Setting the value to NA means that the value is not fixed. Is passed on to autofitVariogram.
# The nugget is the y-intercept of the variogram. In practical terms, the nugget represents the small-scale variability of the data. A portion of that short range variability can be the result of measurement error. 
# The range is the distance after which the variogram levels off. The physical meaning of the range is that pairs of points that are this distance or greater apart are not spatially correlated. 
# The sill is the total variance contribution, or the maximum variability between pairs of points. 

# increasing the range gave better fit than auto
d15N.RK.auto <- autoKrige(d15N ~ 1, krig.RK, Grid.RK, fix.value=c(NA, 2, NA)) # ordinary kriging
plot(d15N.RK.auto, sp.layout = list(pts = list("sp.points", krig.RK)))

#d15N.RK.auto$krige_output

# make to dataframes for lm, combine
RK.pred.N <- d15N.RK.auto[1] %>% as.data.frame() # model predictions
RK.df.N <- krig.RK %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
# longest axis here is y
pred.RK.df.N<- left_join(RK.df.N, RK.pred.N, by = c("x.meter"="krige_output.x"))
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.RK.df.N)
summary(mod) #R squared = 0.21
mean(pred.RK.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 4.9 d15N
mean(pred.RK.df.N$krige_output.var1.stdev, na.rm=T) # 1.9

# inspect model
# plot(pred.RK.df.N$krige_output.var1.pred ~ pred.RK.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

#predicted krige
plotd15N.krig.RK<-spplot(d15N.RK.auto$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", krig.RK, pch=c(16,17,1)[krig.RK$Sample], 
                        col="black", cex=0.5, alpha=0.5), 
       main=list(label=expression(paste(delta^{15}, N, " - RK (Remnant Forest)")), cex=0.7))

combine the KP-RK d15N pooled isoscape

#####################
grid.draw.ggmatrix <- function(x, recording = TRUE) {
  print(x)
}
### combined KP-Rk krig d15N plot 
par(mfrow=c(1,2))
gridExtra::grid.arrange(plotd15N.krig.KP, plotd15N.krig.RK, ncol=2, nrow=1, widths = c(1.2,1))

dev.copy(png, "figures/FigS2_ab.d15N.isoscape.png", width = 8, height = 4, units = 'in', res = 300)
dev.off()

δ13C pooled isoscape

setup

################# d13C krigs
################# make site maps based on bubble plots

KP.map<-krig.KP %>% as.data.frame %>% 
  ggplot(aes(x.meter, y.meter, group=Sample)) + geom_point(aes(size=d13C, color=Sample), alpha=3/4) + 
  ggtitle("KP plot--d13C (permil)") + coord_equal() + theme_bw()


RK.map<-krig.RK %>% as.data.frame %>% 
  ggplot(aes(x.meter, y.meter, group=Sample)) + geom_point(aes(size=d13C, color=Sample), alpha=3/4) +
  ggtitle("RK plot--d13C (permil)") + coord_equal() + theme_bw()

plot_grid(RK.map, KP.map, ncol=2, nrow=1)

dev.copy(pdf, "figures/notused/dot.scape.d13C.pdf", width=9, height=4, encod="MacRoman")
dev.off()

#####################
#####################

Acacia koa plantation (KP) d13C isoscape

# autokrige
d13C.KP.auto <- autoKrige(d13C ~ 1, krig.KP, Grid.KP) # ordinary kriging
plot(d13C.KP.auto, sp.layout = list(pts = list("sp.points", krig.KP)))

#d13C.KP.auto$krige_output

# make to dataframes for lm, combine
KP.pred.C <- d13C.KP.auto[1] %>% as.data.frame() # model predictions
KP.df.C <- krig.KP %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.KP.df.C<- left_join(KP.df.C, KP.pred.C, by = c("x.meter"="krige_output.x")) # longest axis is x
mod <- lm(krige_output.var1.pred ~ d13C, data=pred.KP.df.C)
summary(mod) #R squared = 0.24

mean(pred.KP.df.C$krige_output.var1.pred, na.rm=T) # mean of predictions -25.9 d13C
mean(pred.KP.df.C$krige_output.var1.stdev, na.rm=T) # 2.3

# inspect model
# plot(pred.KP.df.C$krige_output.var1.pred ~ pred.KP.df.C$d13C, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

# map in automap
#automapPlot(d13C.KP.auto$krige_output, "var1.pred", sp.layout = list("sp.points", krig.KP, pch=16, col="gray20", cex=0.5), col.regions=my.palette)

# map in ssplot
# variance
# spplot(d13C.KP.auto$krige_output,"var1.stdev")

#predicted krige
my.palette4 <- colorRampPalette(c("firebrick1", "paleturquoise2", "azure1"))(4)
col.scheme.C <- colorRampPalette(my.palette4)


plotd13C.krig.KP<-spplot(d13C.KP.auto$krige_output["var1.pred"], col.regions=col.scheme.C, 
       sp.layout = list("sp.points", krig.KP, pch=c(16,17,1)[krig.KP$Sample],
                        col="black", cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{13}, C, " - KP (Restored Forest)")), cex=0.8), colorkey=FALSE)


###########################

Remnant Forest (RK) d13C isoscape: Figure 4cd

###########################
# RK Site Krig
###########################
## Krig RK site 

# autokrige
d13C.RK.auto <- autoKrige(d13C ~ 1, krig.RK, Grid.RK, fix.value=c(NA, 1, NA)) # ordinary kriging
plot(d13C.RK.auto, sp.layout = list(pts = list("sp.points", krig.RK)))

#d13C.RK.auto$krige_output

# make to dataframes for lm, combine
RK.pred.C <- d13C.RK.auto[1] %>% as.data.frame() # model predictions
RK.df.C <- krig.RK %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
# longest axis here is y
pred.RK.df.C<- left_join(RK.df.C, RK.pred.C, by = c("x.meter"="krige_output.x"))
mod <- lm(krige_output.var1.pred ~ d13C, data=pred.RK.df.C)
summary(mod) #R squared = 0.33

mean(pred.RK.df.C$krige_output.var1.pred, na.rm=T) # mean of predictions -27.6 d13C
mean(pred.RK.df.C$krige_output.var1.stdev, na.rm=T) # 2.8

# inspect model
# plot(pred.RK.df.C$krige_output.var1.pred ~ pred.RK.df.C$d13C, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# map in automap
#automapPlot(d13C.RK.auto$krige_output, "var1.pred", sp.layout = list("sp.points", krig.RK), col.regions=my.palette)

# variance
# spplot(d13C.RK.auto$krige_output,"var1.stdev")

#predicted krige
plotd13C.krig.RK<-spplot(d13C.RK.auto$krige_output["var1.pred"], col.regions=col.scheme.C, 
       sp.layout = list("sp.points", krig.RK, pch=c(16,17,1)[krig.RK$Sample],
                        col="black", cex=0.5, alpha=0.5), 
       main=list(label=expression(paste(delta^{13}, C, " - RK (Remnant Forest)")), cex=0.7))

combine the plots

#####################
grid.draw.ggmatrix <- function(x, recording = TRUE) {
  print(x)
}
### combined KP-Rk krig d13C plot 
par(mfrow=c(1,2))
gridExtra::grid.arrange(plotd13C.krig.KP,plotd13C.krig.RK, ncol=2, nrow=1, widths = c(1.2,1))

dev.copy(png, "figures/FigS2_cd.d13C.isoscape.png", width = 8, height = 4, units = 'in', res = 300)
dev.off()

Density plots: pooled samples

Density plots using predictions of N and C values for all sample types: the soil, koa, and Rubus.

###################
# make density plots using predictions
# combine the predictions for each plot
KP.df.out.N<-as.data.frame(KP.pred.N$krige_output.var1.pred); KP.df.out.N$Plot<-"KP"
RK.df.out.N<-as.data.frame(RK.pred.N$krige_output.var1.pred); RK.df.out.N$Plot<-"RK"; 
colnames(KP.df.out.N)<-c("d15N.pred", "Plot")
colnames(RK.df.out.N)<-c("d15N.pred", "Plot")

# new dataframe
pred.dat.N<-rbind(KP.df.out.N, RK.df.out.N)
pred.dat.N$Plot<-as.factor(pred.dat.N$Plot)
pred.dat.N %>% 
  group_by(Plot) %>%
  summarise(no_rows = length(Plot))

#man whitney for significance (not normal data)
mwu(pred.dat.N, d15N.pred, Plot) # signif difference in predictions (p<0.001)

# Density plot

# plot.means
predict.mean.N <- ddply(pred.dat.N, "Plot", summarise, grp.mean=mean(d15N.pred, na.rm=TRUE))
predict.SD.N <- ddply(pred.dat.N, "Plot", summarise, sd=sd(d15N.pred, na.rm=TRUE))


density.predict.N.pooled<-ggplot(pred.dat.N, aes(x=d15N.pred)) +
  geom_density(aes(color=Plot, fill=Plot), alpha=0.5, lwd=0.4)+
  xlab(expression(paste("Soil+Foliar ",delta^{15}, N["predicted"], sp="")))+
  theme(axis.text = element_text(size = 6), axis.ticks = element_line(size = 0.2)) +
  ylab("density")+
  scale_y_continuous(labels = label_number(accuracy = 0.5))+
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  geom_vline(data=predict.mean.N, aes(xintercept=grp.mean, color=Plot),
             linetype="dashed", lwd=0.2) + BW.back2
  #annotate(geom="text", x=0, y=3.3, label=expression(paste(bold("A"))), size=3) 


######## Carbon


###################
# make density plots using predictions
# combine the predictions for each plot
KP.df.out.C<-as.data.frame(KP.pred.C$krige_output.var1.pred); KP.df.out.C$Plot<-"KP"
RK.df.out.C<-as.data.frame(RK.pred.C$krige_output.var1.pred); RK.df.out.C$Plot<-"RK"; 
colnames(KP.df.out.C)<-c("d13C.pred", "Plot")
colnames(RK.df.out.C)<-c("d13C.pred", "Plot")

# new dataframe
pred.dat.C<-rbind(KP.df.out.C, RK.df.out.C)
pred.dat.C$Plot<-as.factor(pred.dat.C$Plot)
pred.dat.C %>% 
  group_by(Plot) %>%
  summarise(no_rows = length(Plot))

#man whitney for significance (not normal data)
mwu(pred.dat.C, d13C.pred, Plot) # signif difference in predictions (p<0.001)

# Density plot
# plot.means
predict.mean.C <- ddply(pred.dat.C, "Plot", summarise, grp.mean=mean(d13C.pred, na.rm=TRUE))
predict.sd.C <- ddply(pred.dat.C, "Plot", summarise, sd=sd(d13C.pred, na.rm=TRUE))

density.predict.C.pooled<-ggplot(pred.dat.C, aes(x=d13C.pred)) +
  geom_density(aes(color=Plot, fill=Plot), alpha=0.5, lwd=0.4)+
  xlab(expression(paste("Soil+Foliar ", delta^{13}, C["predicted"], sp="")))+
  theme(axis.text = element_text(size = 6), axis.ticks = element_line(size = 0.2)) +
  ylab("")+
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  geom_vline(data=predict.mean.C, aes(xintercept=grp.mean, color=Plot),
             linetype="dashed", lwd=0.2) + BW.back2 
  #annotate(geom="text", x=-32, y=1.7, label=expression(paste(bold("B"))), size=3)

# get the legend, # create some space to the left of the legend
density.legend <- get_legend(
  density.predict.C.pooled + #plot this one
    theme(legend.title=element_blank())+ # no need for a title above legend
    theme(legend.box.margin = margin(0, 0, 0, 12)) + #box margin
    theme(legend.key.size = unit(0.3, "cm"))) # legend size

gridExtra::grid.arrange(density.predict.N.pooled + theme(legend.position = "none"),
                        density.predict.C.pooled + theme(legend.position = "none"),
                        density.legend,
                        ncol=3, nrow=1, widths = c(1,1,0.4))

Soil isoscapes

δ15N soil-isoscape

Subset data and only examine SOIL.
Restored forest (KP) and Remnant Forest (RK)

###### KP site d15N

## d15N SOIL plot
krig.KP<- scape.data %>% filter(Plot=="KP") # just KP
KP.soil<-  krig.KP[(krig.KP$Sample=="Soil"),] #just soil
KP.soil$Sample<-droplevels(KP.soil$Sample)

## Krig KP sites
coordinates(KP.soil)<- ~x.meter + y.meter

# Create a grid of "Pixels" using x as columns and y as rows
# And the rows and columns of pixels:
Columns=seq(from=-1, to=36, by=0.05)
Rows=seq(from=-1, to=21, by=0.05)
Grid.KP <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.KP) <- ~ x+y
gridded(Grid.KP) <- TRUE # Plot the grid and points

## expand binding box 
#KP.soil@bbox # current data binding box
x<-c(-1, 36)
y<-c(-1, 21)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
KP.soil@bbox<-bbox(S) # expanded binding box for data
Grid.KP@bbox<-bbox(S) # expand for plot corner

# autokrige
d15N.KP.soil <- autoKrige(d15N ~ 1, KP.soil, Grid.KP) # ordinary kriging
plot(d15N.KP.soil, sp.layout = list(pts = list("sp.points", KP.soil)))

#d15N.KP.soil$krige_output

# make to dataframes for lm, combine
KP.soil.pred.N <- d15N.KP.soil[1] %>% as.data.frame() # model predictions
KP.soil.df.N <- KP.soil %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.KP.soil.df.N<- left_join(KP.soil.df.N, KP.soil.pred.N, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.KP.soil.df.N)
summary(mod) #R squared = 0.015

mean(pred.KP.soil.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 6.0 d15N
mean(pred.KP.soil.df.N$krige_output.var1.stdev, na.rm=T) # 0.35

# inspect model
# plot(pred.KP.soil.df.N$krige_output.var1.pred ~ pred.KP.soil.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

########### plot to diagnostic variogram
#predicted krige
plotd15N.krig.KP.soil<-spplot(d15N.KP.soil$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", KP.soil, pch=1, 
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{15}, N, " - KP (Restored Forest)")), cex=0.8), colorkey=FALSE)

RK soil isoscape

###########################
# RK Site Krig
###########################

## d15N SOIL plot
krig.RK<- scape.data %>% filter(Plot=="RK") # just KP
RK.soil<-  krig.RK[(krig.RK$Sample=="Soil"),] #just soil
RK.soil$Sample<-droplevels(RK.soil$Sample)

## Krig RK sites
coordinates(RK.soil)<- ~x.meter + y.meter

# Create a grid of "Pixels" using x as columns and y as rows
# And the rows and columns of pixels:
Columns=seq(from=-1, to=21, by=0.05)
Rows=seq(from=-1, to=36, by=0.05)
Grid.RK <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.RK) <- ~ x+y
gridded(Grid.RK) <- TRUE # Plot the grid and points

## expand binding box 
#RK.soil@bbox # current data binding box
x<-c(-1, 21)
y<-c(-1, 36)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
RK.soil@bbox<-bbox(S) # expanded binding box for data
Grid.RK@bbox<-bbox(S) # expand for plot corner

# autokrige
d15N.RK.soil <- autoKrige(d15N ~ 1, RK.soil, Grid.RK) # ordinary kriging
plot(d15N.RK.soil, sp.layout = list(pts = list("sp.points", RK.soil)))

#d15N.RK.soil$krige_output

# make to dataframes for lm, combine
RK.soil.pred.N <- d15N.RK.soil[1] %>% as.data.frame() # model predictions
RK.soil.df.N <- RK.soil %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.RK.soil.df.N<- left_join(RK.soil.df.N, RK.soil.pred.N, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.RK.soil.df.N)
summary(mod) #R squared = 0.01

mean(pred.RK.soil.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 6.4 d15N
mean(pred.RK.soil.df.N$krige_output.var1.stdev, na.rm=T) # 0.8

# inspect model
# plot(pred.RK.soil.df.N$krige_output.var1.pred ~ pred.RK.soil.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")


#predicted krige
plotd15N.krig.RK.soil<-spplot(d15N.RK.soil$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", RK.soil, pch=1, 
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{15}, N, " - RK (Remnant Forest)")), cex=0.8), colorkey=TRUE)

combine the soil isoscapes

#####################
grid.draw.ggmatrix <- function(x, recording = TRUE) {
  print(x)
}
### combined KP-Rk krig d15N plot 
par(mfrow=c(1,2))
gridExtra::grid.arrange(plotd15N.krig.KP.soil, plotd15N.krig.RK.soil, ncol=2, nrow=1, widths = c(1.2,1))

dev.copy(png, "figures/Fig5_ab.d15N.soil.isoscape.png", width = 8, height = 4, units = 'in', res = 300)
dev.off()

δ13C soil-isoscape

soil isotopes, first the restored site then the remnant site

###### KP site d13C

# autokrige
d13C.KP.soil <- autoKrige(d13C ~ 1, KP.soil, Grid.KP) # ordinary kriging
plot(d13C.KP.soil, sp.layout = list(pts = list("sp.points", KP.soil)))

#d13C.KP.soil$krige_output

# make to dataframes for lm, combine
KP.soil.pred.C <- d13C.KP.soil[1] %>% as.data.frame() # model predictions
KP.soil.df.C <- KP.soil %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.KP.soil.df.C<- left_join(KP.soil.df.C, KP.soil.pred.C, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d13C, data=pred.KP.soil.df.C)
summary(mod) #R squared = 0.008

mean(pred.KP.soil.df.C$krige_output.var1.pred, na.rm=T) # mean of predictions -24.4 d13C
mean(pred.KP.soil.df.C$krige_output.var1.stdev, na.rm=T) # 0.6

# inspect model
# plot(pred.KP.soil.df.C$krige_output.var1.pred ~ pred.KP.soil.df.C$d13C, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

# map in automap
#automapPlot(d13C.KP.soil$krige_output, "var1.pred", sp.layout = list("sp.points", KP.soil, pch=16, col="gray20", cex=0.5), col.regions=my.palette)

# map in ssplot
# variance
# spplot(d13C.KP.soil$krige_output,"var1.stdev")

#predicted krige
plotd13C.krig.KP.soil<-spplot(d13C.KP.soil$krige_output["var1.pred"], col.regions=col.scheme.C, 
       sp.layout = list("sp.points", KP.soil, pch=1, 
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{13}, C, " - KP (Restored Forest)")), cex=0.8), colorkey=FALSE)



###########################
# RK Site Krig
###########################

# autokrige
d13C.RK.soil <- autoKrige(d13C ~ 1, RK.soil, Grid.RK) # ordinary kriging
plot(d13C.RK.soil, sp.layout = list(pts = list("sp.points", RK.soil)))

#d13C.RK.soil$krige_output

# make to dataframes for lm, combine
RK.soil.pred.C <- d13C.RK.soil[1] %>% as.data.frame() # model predictions
RK.soil.df.C <- RK.soil %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.RK.soil.df.C<- left_join(RK.soil.df.C, RK.soil.pred.C, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d13C, data=pred.RK.soil.df.C)
summary(mod) #R squared = 0.16

mean(pred.RK.soil.df.C$krige_output.var1.pred, na.rm=T) # mean of predictions 4.4 d13C
mean(pred.RK.soil.df.C$krige_output.var1.stdev, na.rm=T) # 2.1

# inspect model
# plot(pred.RK.soil.df.C$krige_output.var1.pred ~ pred.RK.soil.df.C$d13C, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

# map in automap
#automapPlot(d13C.RK.soil$krige_output, "var1.pred", sp.layout = list("sp.points", RK.soil, pch=16, col="gray20", cex=0.5), col.regions=my.palette)

# map in ssplot
# variance
# spplot(d13C.RK.soil$krige_output,"var1.stdev")

#predicted krige
plotd13C.krig.RK.soil<-spplot(d13C.RK.soil$krige_output["var1.pred"], col.regions=col.scheme.C, 
       sp.layout = list("sp.points", RK.soil, pch=1, 
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{13}, C, " - RK (Remnant Forest)")), cex=0.8), colorkey=TRUE)


#####################
grid.draw.ggmatrix <- function(x, recording = TRUE) {
  print(x)
}
### combined KP-Rk krig d13C plot 
par(mfrow=c(1,2))
gridExtra::grid.arrange(plotd13C.krig.KP.soil, plotd13C.krig.RK.soil, ncol=2, nrow=1, widths = c(1.2,1))

dev.copy(png, "figures/Fig5_cd.d13C.isoscape.soils.png", width = 8, height = 4, units = 'in', res = 300)
dev.off()

Density plots for soil isoscapes

# make density plots using predictions
# combine the predictions for each plot


############## Nitrogen plot
KP.df.soil.N<-as.data.frame(pred.KP.soil.df.N$krige_output.var1.pred); KP.df.soil.N$Plot<-"KP"
RK.df.soil.N<-as.data.frame(pred.RK.soil.df.N$krige_output.var1.pred); RK.df.soil.N$Plot<-"RK" 
colnames(KP.df.soil.N)<-c("d15N.pred", "Plot")
colnames(RK.df.soil.N)<-c("d15N.pred", "Plot")

# new dataframe
pred.soil.N<-rbind(KP.df.soil.N, RK.df.soil.N)
pred.soil.N$Plot<-as.factor(pred.soil.N$Plot)
pred.soil.N %>% 
  group_by(Plot) %>%
  summarise(no_rows = length(Plot))

#man whitney for significance (not normal data)
mwu(pred.soil.N, d15N.pred, Plot) # signif difference in predictions (p<0.001)

# Density plot
# plot.means
predict.mean.N <- ddply(pred.soil.N, "Plot", summarise, grp.mean=mean(d15N.pred, na.rm=TRUE))
predict.sd.N <- ddply(pred.soil.N, "Plot", summarise, sd=sd(d15N.pred, na.rm=TRUE))

density.predict.Nsoil<-ggplot(pred.soil.N, aes(x=d15N.pred)) +
  geom_density(aes(color=Plot, fill=Plot), alpha=0.5, lwd=0.4)+ ylim(0,1.2) +
  scale_y_continuous(labels = label_number(accuracy = 0.3))+
  xlab(expression(paste("Soil ",delta^{15}, N["predicted"], sp="")))+
  theme(axis.text = element_text(size = 6), axis.ticks = element_line(size = 0.2)) +
  ylab("density")+
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  geom_vline(data=predict.mean.N, aes(xintercept=grp.mean, color=Plot),
             linetype="dashed", lwd=0.2) + BW.back2 
  #annotate(geom="text", x=2, y=1.2, label=expression(paste(bold("C"))), size=3)


############## Carbon
KP.df.soil.C<-as.data.frame(pred.KP.soil.df.C$krige_output.var1.pred); KP.df.soil.C$Plot<-"KP"
RK.df.soil.C<-as.data.frame(pred.RK.soil.df.C$krige_output.var1.pred); RK.df.soil.C$Plot<-"RK" 
colnames(KP.df.soil.C)<-c("d13C.pred", "Plot")
colnames(RK.df.soil.C)<-c("d13C.pred", "Plot")

# new dataframe
pred.soil.C<-rbind(KP.df.soil.C, RK.df.soil.C)
pred.soil.C$Plot<-as.factor(pred.soil.C$Plot)
pred.soil.C %>% 
  group_by(Plot) %>%
  summarise(no_rows = length(Plot))

#man whitney for significance (not normal data)
mwu(pred.soil.C, d13C.pred, Plot) # signif difference in predictions (p<0.001)

# Density plot
# plot.means
predict.mean.C <- ddply(pred.soil.C, "Plot", summarise, grp.mean=mean(d13C.pred, na.rm=TRUE))

density.predict.Csoil<-ggplot(pred.soil.C, aes(x=d13C.pred)) +
  geom_density(aes(color=Plot, fill=Plot), alpha=0.5, lwd=0.4)+ ylim(0,0.8) +
  xlab(expression(paste("Soil ",delta^{13}, C["predicted"], sp="")))+
  ylab("")+
  theme(axis.text = element_text(size = 6), axis.ticks = element_line(size = 0.2)) +
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  geom_vline(data=predict.mean.C, aes(xintercept=grp.mean, color=Plot),
             linetype="dashed", lwd=0.2) + BW.back2 
  #annotate(geom="text", x=-28, y=0.8, label=expression(paste(bold("D"))), size=3)

gridExtra::grid.arrange(density.predict.Nsoil + theme(legend.position = "none"),
                        density.predict.Csoil + theme(legend.position = "none"),
                        density.legend,
                        ncol=3, nrow=1, widths = c(1,1,0.3))

Foliar Isoscapes

δ15N foliar-isoscape

Subset data and only examine plants.
- Restored forest (KP) and Remnant Forest (RK)

Plant-isoscape: Restored forest and remnant forest (Plant isoscape: d15N, Figure S5).
Koa Plantation:

#### d15N Plants isoscape

## d15N plants plot
krig.KP<- scape.data %>% filter(Plot=="KP") # just KP
KP.plants<-  krig.KP[!(krig.KP$Sample=="Soil"),] #just plants, remove the soil
KP.plants$Sample<-droplevels(KP.plants$Sample)

## Krig KP sites
coordinates(KP.plants)<- ~x.meter + y.meter

# Create a grid of "Pixels" using x as columns and y as rows
# And the rows and columns of pixels:
Columns=seq(from=-1, to=36, by=0.05)
Rows=seq(from=-1, to=21, by=0.05)
Grid.KP <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.KP) <- ~ x+y
gridded(Grid.KP) <- TRUE # Plot the grid and points

## expand binding box 
#KP.plants@bbox # current data binding box
x<-c(-1, 36)
y<-c(-1, 21)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
KP.plants@bbox<-bbox(S) # expanded binding box for data
Grid.KP@bbox<-bbox(S) # expand for plot corner

# autokrige
d15N.KP.plants <- autoKrige(d15N ~ 1, KP.plants, Grid.KP, fix.value=c(0.2, 3, 0.6)) # ordinary kriging

############## diagnostics
plot(d15N.KP.plants, sp.layout = list(pts = list("sp.points", KP.plants)))

#d15N.KP.plants$krige_output

# make to dataframes for lm, combine
KP.plants.pred.N <- d15N.KP.plants[1] %>% as.data.frame() # model predictions
KP.plants.df.N <- KP.plants %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.KP.plants.df.N<- left_join(KP.plants.df.N, KP.plants.pred.N, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.KP.plants.df.N)
summary(mod) #R squared = 0.19

mean(pred.KP.plants.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 1.6 d15N
mean(pred.KP.plants.df.N$krige_output.var1.stdev, na.rm=T) # 0.7

# inspect model
# plot(pred.KP.plants.df.N$krige_output.var1.pred ~ pred.KP.plants.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")

#predicted krige
plotd15N.krig.KP.plants<-spplot(d15N.KP.plants$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", KP.plants, pch=c(16,17)[KP.plants$Sample],
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{15}, N, " - KP (Restored Forest)")), cex=0.8), colorkey=FALSE)

#plotd15N.krig.KP.plants

Remnant Koa forest

###########################
# RK Site Krig
###########################

## d15N plants plot
krig.RK<- scape.data %>% filter(Plot=="RK") # just KP
RK.plants<-  krig.RK[!(krig.RK$Sample=="Soil"),] #just plants, remove soil
RK.plants$Sample<-droplevels(RK.plants$Sample)

## Krig RK sites
coordinates(RK.plants)<- ~x.meter + y.meter

# Create a grid of "Pixels" using x as columns and y as rows
# And the rows and columns of pixels:
Columns=seq(from=-1, to=21, by=0.05)
Rows=seq(from=-1, to=36, by=0.05)
Grid.RK <- expand.grid(x=Columns,y=Rows)
coordinates(Grid.RK) <- ~ x+y
gridded(Grid.RK) <- TRUE # Plot the grid and points

## expand binding box 
#RK.plants@bbox # current data binding box
x<-c(-1, 21)
y<-c(-1, 36)
xy<-cbind(x,y)
S<-SpatialPoints(xy)
bbox(S)
RK.plants@bbox<-bbox(S) # expanded binding box for data
Grid.RK@bbox<-bbox(S) # expand for plot corner

# autokrige
d15N.RK.plants <- autoKrige(d15N ~ 1, RK.plants, Grid.RK) # ordinary kriging
plot(d15N.RK.plants, sp.layout = list(pts = list("sp.points", RK.plants)))

#d15N.RK.plants$krige_output

# make to dataframes for lm, combine
RK.plants.pred.N <- d15N.RK.plants[1] %>% as.data.frame() # model predictions
RK.plants.df.N <- RK.plants %>% as.data.frame() # dataframe

# make dataframe with data and predictions (krig) to assess fit
pred.RK.plants.df.N<- left_join(RK.plants.df.N, RK.plants.pred.N, by = c("x.meter"="krige_output.x"))#longest axis is x
mod <- lm(krige_output.var1.pred ~ d15N, data=pred.RK.plants.df.N)
summary(mod) #R squared = 0.15

mean(pred.RK.plants.df.N$krige_output.var1.pred, na.rm=T) # mean of predictions 2.8 d15N
mean(pred.RK.plants.df.N$krige_output.var1.stdev, na.rm=T) # 0.5

# inspect model
# plot(pred.RK.plants.df.N$krige_output.var1.pred ~ pred.RK.plants.df.N$d15N, xlab = "Observed", ylab = "Predicted", cex=0.2); abline(0,1, lty=2); abline(mod, col = "blue")

# Adding the sp.layout parameter shows the locations of the measurements
my.palette <- brewer.pal(n = 9, name = "RdBu")


#predicted krige
plotd15N.krig.RK.plants<-spplot(d15N.RK.plants$krige_output["var1.pred"], col.regions=col.scheme.N, 
       sp.layout = list("sp.points", RK.plants, pch=c(16,17)[RK.plants$Sample],
                        col=c("black"), cex=0.5, alpha=0.5),
       main=list(label=expression(paste(delta^{15}, N, " - RK (Remnant Forest)")), cex=0.8), colorkey=TRUE)
#plotd15N.krig.RK.plants

combine the two plant-isoscapes

#####################
grid.draw.ggmatrix <- function(x, recording = TRUE) {
  print(x)
}
### combined KP-Rk krig d15N plot 
par(mfrow=c(1,2))
gridExtra::grid.arrange(plotd15N.krig.KP.plants, plotd15N.krig.RK.plants, ncol=2, nrow=1, widths = c(1.2,1))

dev.copy(png, "figures/Fig 6_ab.d15N.isoscape.plants.png", width = 8, height = 4, units = 'in', res = 300)
dev.off()

Density plots showing the distribution of all extrapolated points. Plant-isoscape: density plot for the d15N-predicted values for the plant-only (foliar) isoscape

# make density plots using predictions
# combine the predictions for each plot

############## Nitrogen plot
KP.df.plants.N<-as.data.frame(pred.KP.plants.df.N$krige_output.var1.pred); KP.df.plants.N$Plot<-"KP"
RK.df.plants.N<-as.data.frame(pred.RK.plants.df.N$krige_output.var1.pred); RK.df.plants.N$Plot<-"RK" 
colnames(KP.df.plants.N)<-c("d15N.pred", "Plot")
colnames(RK.df.plants.N)<-c("d15N.pred", "Plot")

# new dataframe
pred.plants.N<-rbind(KP.df.plants.N, RK.df.plants.N)
pred.plants.N$Plot<-as.factor(pred.plants.N$Plot)
pred.plants.N %>% 
  group_by(Plot) %>%
  summarise(no_rows = length(Plot))

#man whitney for significance (not normal data)
mwu(pred.plants.N, d15N.pred, Plot) # signif difference in predictions (p<0.001)

### Density plot

# plot.means
predict.mean.N <- ddply(pred.plants.N, "Plot", summarise, grp.mean=mean(d15N.pred, na.rm=TRUE))
predict.SD.N <- ddply(pred.plants.N, "Plot", summarise, sd=sd(d15N.pred, na.rm=TRUE))

density.predict.Nplants<-ggplot(pred.plants.N, aes(x=d15N.pred)) +
  geom_density(aes(color=Plot, fill=Plot), alpha=0.5, lwd=0.4)+ ylim(0,2.5) +
  xlab(expression(paste("Foliar ", delta^{15}, N["predicted"], sp="")))+
  theme(axis.text = element_text(size = 6), axis.ticks = element_line(size = 0.2))+
  scale_color_manual(values=c("#E69F00", "#56B4E9")) +
  scale_fill_manual(values=c("#E69F00", "#56B4E9")) +
  #annotate(geom="text", x=0, y=2.5, label=expression(paste(bold("E"))), size=3) +
  geom_vline(data=predict.mean.N, aes(xintercept=grp.mean, color=Plot),
             linetype="dashed", lwd=0.2) + BW.back2
### group all density plots

fig.format3<-theme(panel.grid.major = element_blank(), 
                   panel.grid.minor = element_blank(),
                   panel.background = element_blank(), 
                   axis.line = element_line(colour = "black", size=0.2), 
                   text = element_text(size = 6))


plot_grid((density.predict.N.pooled  + ylab("density") + 
             theme(legend.position = "none")+ fig.format3),
          
          (density.predict.C.pooled + ylab("") + 
             theme(legend.position = c(0.85, 0.85), legend.key.size = unit(0.3, "cm"),
                   legend.title = element_blank())+fig.format3),
          
          (density.predict.Nsoil + ylab("density") + 
             theme(legend.position = "none") +fig.format3),
          
          (density.predict.Csoil + ylab("")+ theme(legend.position = "none")+fig.format3),
          
          (density.predict.Nplants + theme(legend.position = "none")+fig.format3),
          
          labels=c('A', 'B', 'C', 'D', 'E'), label_size=8, hjust=-1, vjust= 2, ncol=2, nrow=3)

dev.copy(pdf, "figures/Fig 4_ad_density plots.pdf", width = 3, height = 5)
dev.off()